Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RANBP3 Gene

Aliases for RANBP3 Gene

  • RAN Binding Protein 3 2 3 5
  • Ran-Binding Protein 3 3
  • RanBP3 4

External Ids for RANBP3 Gene

Previous GeneCards Identifiers for RANBP3 Gene

  • GC19M006008
  • GC19M005856
  • GC19M005867
  • GC19M005675

Summaries for RANBP3 Gene

Entrez Gene Summary for RANBP3 Gene

  • This gene encodes a protein with a RanBD1 domain that is found in both the nucleus and cytoplasm. This protein plays a role in nuclear export as part of a heteromeric complex. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for RANBP3 Gene

RANBP3 (RAN Binding Protein 3) is a Protein Coding gene. Among its related pathways are Cytoskeletal Signaling and HTLV-I infection. Gene Ontology (GO) annotations related to this gene include Ran GTPase binding and R-SMAD binding. An important paralog of this gene is RANBP3L.

UniProtKB/Swiss-Prot for RANBP3 Gene

  • Acts as a cofactor for XPO1/CRM1-mediated nuclear export, perhaps as export complex scaffolding protein. Bound to XPO1/CRM1, stabilizes the XPO1/CRM1-cargo interaction. In the absence of Ran-bound GTP prevents binding of XPO1/CRM1 to the nuclear pore complex. Binds to CHC1/RCC1 and increases the guanine nucleotide exchange activity of CHC1/RCC1. Recruits XPO1/CRM1 to CHC1/RCC1 in a Ran-dependent manner. Negative regulator of TGF-beta signaling through interaction with the R-SMAD proteins, SMAD2 and SMAD3, and mediating their nuclear export.

Gene Wiki entry for RANBP3 Gene

Additional gene information for RANBP3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RANBP3 Gene

Genomics for RANBP3 Gene

GeneHancer (GH) Regulatory Elements for RANBP3 Gene

Promoters and enhancers for RANBP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J005976 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.2 -200 3.5 HDGF MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 LOC100128568 RANBP3 CAPS DUS3L ENSG00000267571 NDUFA11 VMAC SAFB GPR108 FUT5
GH19J006527 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 77.2 -552.3 -552335 6.2 YBX1 IRF4 E2F8 ZNF143 ZNF548 MCM3 SP3 MEF2D ZNF610 GLIS1 TNFSF9 ZNF557 KHSRP DUS3L SAFB SAFB2 SNRPEP4 ENSG00000267571 RANBP3 GTF2F1
GH19J005689 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 58.2 +286.2 286207 5 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 ZC3H11A RPL36 DUS3L KHSRP SAFB ENSG00000267571 SNRPEP4 SAFB2 VMAC RANBP3 KDM4B
GH19J006371 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 32.3 -395.0 -394993 3.4 HDGF FOXA2 PKNOX1 SMAD1 ARNT ZFP64 SIN3A FEZF1 DMAP1 ZNF2 ALKBH7 KHSRP DUS3L ZNF557 SAFB RANBP3 SNRPEP4 GTF2F1 SAFB2 TRIP10
GH19J005679 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 31.2 +297.9 297870 2.5 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 HSD11B1L C19orf70 DUS3L SAFB KHSRP ENSG00000267571 KDM4B RANBP3 SAFB2 GTF2F1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RANBP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RANBP3 gene promoter:
  • COUP-TF
  • COUP
  • COUP-TF1
  • HNF-4alpha2

Genomic Locations for RANBP3 Gene

Genomic Locations for RANBP3 Gene
chr19:5,916,139-5,978,309
(GRCh38/hg38)
Size:
62,171 bases
Orientation:
Minus strand
chr19:5,916,150-5,978,320
(GRCh37/hg19)
Size:
62,171 bases
Orientation:
Minus strand

Genomic View for RANBP3 Gene

Genes around RANBP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RANBP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RANBP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RANBP3 Gene

Proteins for RANBP3 Gene

  • Protein details for RANBP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6Z4-RANB3_HUMAN
    Recommended name:
    Ran-binding protein 3
    Protein Accession:
    Q9H6Z4
    Secondary Accessions:
    • B2RAT8
    • O60405
    • O75759
    • O75760
    • Q9BT47
    • Q9UG74

    Protein attributes for RANBP3 Gene

    Size:
    567 amino acids
    Molecular mass:
    60210 Da
    Quaternary structure:
    • Interacts with CHC1 in a Ran-stimulated manner. Interacts with XPO1. Interacts (via its C-terminal R domain) with SMAD2 (dephosphorylated form via its MH1 and MH2 domains); the interaction results in the nuclear export of SMAD2 and termination of the TGF-beta signaling. Interacts (via its C-terminal R domain) with SMAD3 (dephosphorylated form via its MH1 domain); the interaction results in the nuclear export of SMAD3 and termination of the TGF-beta signaling.
    SequenceCaution:
    • Sequence=AAH04349.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=CAB43293.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RANBP3 Gene

    Alternative splice isoforms for RANBP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RANBP3 Gene

Post-translational modifications for RANBP3 Gene

  • Ubiquitination at Lys413
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RANBP3 Gene

Domains & Families for RANBP3 Gene

Gene Families for RANBP3 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for RANBP3 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RANBP3: view

No data available for UniProtKB/Swiss-Prot for RANBP3 Gene

Function for RANBP3 Gene

Molecular function for RANBP3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a cofactor for XPO1/CRM1-mediated nuclear export, perhaps as export complex scaffolding protein. Bound to XPO1/CRM1, stabilizes the XPO1/CRM1-cargo interaction. In the absence of Ran-bound GTP prevents binding of XPO1/CRM1 to the nuclear pore complex. Binds to CHC1/RCC1 and increases the guanine nucleotide exchange activity of CHC1/RCC1. Recruits XPO1/CRM1 to CHC1/RCC1 in a Ran-dependent manner. Negative regulator of TGF-beta signaling through interaction with the R-SMAD proteins, SMAD2 and SMAD3, and mediating their nuclear export.
GENATLAS Biochemistry:
RAN binding protein 3,localized in the nucleus,nuclear effector of the RAN pathway,preferentially bound to importin alpha 3

Phenotypes From GWAS Catalog for RANBP3 Gene

Gene Ontology (GO) - Molecular Function for RANBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 contributes_to GTPase activator activity IBA --
GO:0005515 protein binding IPI 11932251
GO:0008536 Ran GTPase binding IBA --
GO:0070412 R-SMAD binding IPI 19289081
genes like me logo Genes that share ontologies with RANBP3: view
genes like me logo Genes that share phenotypes with RANBP3: view

Animal Model Products

CRISPR Products

miRNA for RANBP3 Gene

miRTarBase miRNAs that target RANBP3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RANBP3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RANBP3 Gene

Localization for RANBP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RANBP3 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RANBP3 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RANBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IBA --
GO:0005813 centrosome IBA --
genes like me logo Genes that share ontologies with RANBP3: view

Pathways & Interactions for RANBP3 Gene

genes like me logo Genes that share pathways with RANBP3: view

Pathways by source for RANBP3 Gene

1 BioSystems pathway for RANBP3 Gene
1 KEGG pathway for RANBP3 Gene
3 Cell Signaling Technology pathways for RANBP3 Gene

SIGNOR curated interactions for RANBP3 Gene

Inactivates:
Other effect:

Gene Ontology (GO) - Biological Process for RANBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle IBA --
GO:0006405 RNA export from nucleus IBA --
GO:0006511 ubiquitin-dependent protein catabolic process IBA --
GO:0006606 protein import into nucleus IBA --
GO:0007051 spindle organization IBA --
genes like me logo Genes that share ontologies with RANBP3: view

Drugs & Compounds for RANBP3 Gene

(3) Drugs for RANBP3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RANBP3: view

Transcripts for RANBP3 Gene

mRNA/cDNA for RANBP3 Gene

Unigene Clusters for RANBP3 Gene

RAN binding protein 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RANBP3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RANBP3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^
SP1: - - - - - - -
SP2: - - - - - - - -
SP3: - - - -
SP4: - - - - - - -
SP5: -
SP6: - - -
SP7: - - - - - - - - - - - - - - - - - - - - - -
SP8: - -
SP9: - - -
SP10: -
SP11:

ExUns: 17a · 17b ^ 18 ^ 19a · 19b · 19c
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:

Relevant External Links for RANBP3 Gene

GeneLoc Exon Structure for
RANBP3
ECgene alternative splicing isoforms for
RANBP3

Expression for RANBP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RANBP3 Gene

Protein differential expression in normal tissues from HIPED for RANBP3 Gene

This gene is overexpressed in Nasal epithelium (23.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RANBP3 Gene



Protein tissue co-expression partners for RANBP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RANBP3 Gene:

RANBP3

SOURCE GeneReport for Unigene cluster for RANBP3 Gene:

Hs.531752

mRNA Expression by UniProt/SwissProt for RANBP3 Gene:

Q9H6Z4-RANB3_HUMAN
Tissue specificity: Widely expressed with high levels in testis and heart.

Evidence on tissue expression from TISSUES for RANBP3 Gene

  • Nervous system(4.7)
  • Intestine(4.3)
  • Eye(4.2)
  • Liver(4.2)
  • Lung(2.8)
  • Adrenal gland(2.5)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with RANBP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RANBP3 Gene

Orthologs for RANBP3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RANBP3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RANBP3 34 33
  • 99.47 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RANBP3 34 33
  • 89.45 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RANBP3 34
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RANBP3 34
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ranbp3 33
  • 79.69 (n)
mouse
(Mus musculus)
Mammalia Ranbp3 16 34 33
  • 79.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RANBP3 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves RANBP3 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.946 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.12030 33
zebrafish
(Danio rerio)
Actinopterygii ranbp3b 34
  • 62 (a)
OneToMany
ranbp3a 34
  • 52 (a)
OneToMany
zgc66385 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3866 33
fruit fly
(Drosophila melanogaster)
Insecta RanBP3 34
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ran-5 34
  • 24 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YRB2 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2235 34
  • 29 (a)
ManyToMany
-- 34
  • 23 (a)
ManyToMany
Species where no ortholog for RANBP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RANBP3 Gene

ENSEMBL:
Gene Tree for RANBP3 (if available)
TreeFam:
Gene Tree for RANBP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RANBP3: view image

Paralogs for RANBP3 Gene

Paralogs for RANBP3 Gene

(11) SIMAP similar genes for RANBP3 Gene using alignment to 18 proteins:

  • RANB3_HUMAN
  • B7Z7F3_HUMAN
  • D6W641_HUMAN
  • F5H4C2_HUMAN
  • K7EID7_HUMAN
  • K7EIJ4_HUMAN
  • K7EJ17_HUMAN
  • K7EJV3_HUMAN
  • K7EMH9_HUMAN
  • K7EMT3_HUMAN
  • K7EN31_HUMAN
  • K7ENB9_HUMAN
  • K7ENJ2_HUMAN
  • K7EPW1_HUMAN
  • K7EQB8_HUMAN
  • K7ERD4_HUMAN
  • K7ESQ0_HUMAN
  • Q53GE1_HUMAN
genes like me logo Genes that share paralogs with RANBP3: view

Variants for RANBP3 Gene

Sequence variations from dbSNP and Humsavar for RANBP3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000082920 -- 5,926,745(-) C/A intron_variant
rs1000111991 -- 5,964,373(-) C/T intron_variant
rs1000144538 -- 5,964,620(-) G/C intron_variant
rs1000176630 -- 5,979,186(-) C/G upstream_transcript_variant
rs1000211866 -- 5,979,506(-) ACAC/AC upstream_transcript_variant

Variation tolerance for RANBP3 Gene

Residual Variation Intolerance Score: 6.46% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.11; 51.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RANBP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RANBP3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RANBP3 Gene

Disorders for RANBP3 Gene

Additional Disease Information for RANBP3

No disorders were found for RANBP3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RANBP3 Gene

Publications for RANBP3 Gene

  1. Human RanBP3, a group of nuclear RanGTP binding proteins. (PMID: 9637251) Mueller L … Ponstingl H (FEBS letters 1998) 2 3 4 22 58
  2. Ran-binding protein 3 links Crm1 to the Ran guanine nucleotide exchange factor. (PMID: 11932251) Nemergut ME … Macara IG (The Journal of biological chemistry 2002) 3 4 22 58
  3. Nuclear export of Smad2 and Smad3 by RanBP3 facilitates termination of TGF-beta signaling. (PMID: 19289081) Dai F … Feng XH (Developmental cell 2009) 3 4 58
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for RANBP3 Gene

Sources for RANBP3 Gene

Content
Loading form....